Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments

Nitrite-dependent anaerobic methane oxidation (n-damo) process uniquely links microbial nitrogen and carbon cycles. Research on n-damo bacteria progresses quickly with experimental evidences through enrichment cultures. Polymerase chain reaction (PCR)-based methods for detecting them in various natural ecosystems and engineered systems play a very important role in the discovery of their distribution, abundance, and biodiversity in the ecosystems. Important characteristics of n-damo enrichments were obtained and their key significance in microbial nitrogen and carbon cycles was investigated. The molecular methods currently used in detecting n-damo bacteria were comprehensively reviewed and discussed for their strengths and limitations in applications with a wide range of samples. The pmoA gene-based PCR primers for n-damo bacterial detection were evaluated and, in particular, several incorrectly stated PCR primer nucleotide sequences in the published papers were also pointed out to allow correct applications of the PCR primers in current and future investigations. Furthermore, this review also offers the future perspectives of n-damo bacteria based on current information and methods available for a better acquisition of new knowledge about this group of bacteria.     

Long-range interactions of <Emphasis Type="Italic">Chara</Emphasis> chloroplasts are sensitive to plasma-membrane H<Superscript>+</Superscript> flows and comprise separate photo- and dark-operated pathways

Local illumination of the characean internode with a 30-s pulse of white light was found to induce the delayed transient increase of modulated chlorophyll fluorescence in shaded cell parts, provided the analyzed region is located downstream in the cytoplasmic flow at millimeter distances from the light spot. The fluorescence response to photostimulation of a remote cell region indicates that the metabolites produced by source chloroplasts in an illuminated region are carried downstream with the cytoplasmic flow, thus ensuring long-distance communications between anchored plastids in giant internodal cells. The properties of individual stages of metabolite signaling are not yet well known. We show here that the export of assimilates and/or reducing equivalents from the source chloroplasts into the flowing cytoplasm is largely insensitive to the direction of plasma-membrane H⁺ flows, whereas the events in sink regions where these metabolites are delivered to the acceptor chloroplasts under dim light are controlled by H⁺ fluxes across the plasma membrane. The fluorescence response to local illumination of remote cell regions was best pronounced under weak background light and was also observed in a modified form within 1–2 min after the transfer of cell to darkness. The fluorescence transients in darkened cells were suppressed by antimycin A, an inhibitor of electron transfer from ferredoxin to plastoquinone, whereas the fluorescence response under background light was insensitive to this inhibitor. We conclude that the accumulation of reduced metabolites in the stroma leads to the reduction of photosystem II primary quinone acceptor (Q_A) via two separate (photochemical and non-photochemical) pathways.     

Impact of updating the non-radiation parameters in the ICRP 103 detriment model

The radiation detriment in ICRP 103 is defined as the product of the organ-specific risk coefficient and the damage that may be associated with a cancer type or hereditary effect. This is used to indicate a weighted risk according to the radiation sensitivity of different organs and the severity of damage that may possibly arise. While the risk refers to radiation exposure parameters, the extent of damage is independent of radiation. The parameters that are not affected by radiation are lethality, impairment of quality of life, and reduced life expectancy, which are considered as quantities associated with the severity of disease or damage. The damage and thus the detriment appear to be mostly affected by lethality, which is the quotient of the age-standardized mortality rate to the incidence rate. The analysis of the detriment presented in this paper focuses on the influence of the lethality on the detriment from 1980 to 2012 in the USA and Germany. While the lethality in this period covering more than three decades has decreased approximately linearly by 30% (both USA and Germany), within the same period the detriment declined only by 13% in the USA and by 15% in Germany. If only based on these two countries, an update on the detriment parameters with reference to 2007, when ICRP 103 was released, would result in a reduced weighted risk, i.e. the radiation detriment would be reduced by 10 to 15% from originally 5.7% per Sv for the whole population to roughly 5% per Sv.     

Returning home after fire: how fire may help us manage the persistence of scrub-steppe specialist bird populations

Semi-natural open habitats have drastically changed in the last few decades due to agricultural intensification and rural depopulation. Steppe-birds, and especially those adapted to primary stages of vegetation succession, are threatened by an increase in scrub cover, and management actions are being applied to reverse scrub encroachment and restore habitat suitability in semi-natural open habitats. In this paper we evaluated for the first time, the long-term effects of a wildfire on habitat structure, vegetation productivity, and the associated response of an endangered scrub-steppe specialist bird, the Dupont’s Lark Chersophilus duponti. Wildfire occurred in a Mediterranean steppe of central Spain dominated by permanent community of dwarf cushions scrubs. Bird abundance was evaluated by line transects in the burnt and unburnt areas 3 years prior to the fire and 4 and 7 years after the fire. We quantified changes in habitat structure at fine scale level through vegetation sampling points and in vegetation productivity by estimating the Normalized Difference Vegetation Index (NDVI). Fire had strong effects for at least up to 4 years after the fire, when lower NDVI values, less scrub cover and fewer, but not significant, number of males were detected in the burnt area with respect to the pre-fire conditions. Seven years after fire most vegetation variables measured did not differ between areas, number of males detected within the burnt area was recovered and NDVI values in burnt area were slightly recovered but were significantly lower than in control area. Slow regeneration of the scrub cover after fire explained the unsuccessful occupation of the burnt area by the Dupont’s Lark up to several years after fire. The more dispersed and shorter habitat created by fire 7 years after the fire seems to be more suitable for the species than that in control areas. The large number of males around the burnt area may have played a role in the recolonization process. In sum, vegetation recovery and the presence of a low scrub-steppe specialist, as the Dupont’s lark, suggests that fire management could be integrated into conservation plans to effectively manage scrub encroachment processes in Mediterranean scrub-steppes.     

The very hungry amphipod: the invasive <Emphasis Type="Italic">Dikerogammarus villosus</Emphasis> shows high consumption rates for two food sources and independent of predator cues

The invasion of the Ponto–Caspian amphipod Dikerogammarus villosus in European rivers is assumed to reduce macroinvertebrate diversity and to alter ecosystem functions. D. villosus shows an extraordinarily flexible feeding behavior including the ability to use various food sources. On the other hand, its response to predation risk seems to depend on environmental factors. To evaluate the ecological function of D. villosus, we estimated the daily food consumption for different food sources and analyzed potential effects of predator avoidance behavior on feeding. D. villosus consumption of willow leaves or chironomid larvae was quantified in 24-h laboratory experiments with and without kairomones of the European bullhead (Cottus gobio). Consumption rates were estimated based on gut content and gut evacuation rate under semi-natural laboratory conditions enabling the animals to feed over the whole time of the evacuation rate experiment. We observed very high evacuation rates and consequently high consumption rates up to 89% of body weight per day. Consumption rates differed significantly between food sources: D. villosus ingested more leaves than chironomid larvae. In contrast, predator cues did not affect the feeding of D. villosus. This might be explained by its strong refuge affinity and probably benefits its successful invasion. A comparison of the estimated consumption rates with results of an own consumption experiment (and other studies) under more artificial conditions indicated that more natural conditions result in higher consumption rates. Consequently, feeding rates from highly artificial experiments should be used with great caution to assess the ecosystem function of D. villosus.     

Hemlock woolly adelgid invasion affects microhabitat characteristics and small mammal communities

Hemlock woolly adelgid (HWA) invasion and preemptive logging practices alter the habitat structure of New England forests and may indirectly affect associated small mammal communities. Microhabitat structure was measured and small mammals were censused in eight large experimental plots to quantify these effects. The Harvard Forest long-term ecological research experiment is a replicated two-block design that includes four ~ 0.81-ha canopy treatments: (1) hemlock control, (2) hardwood control, (3) girdled Treatment, in which hemlock trees were killed by girdling in 2005 and left standing to simulate HWA invasion, and (4) logged treatment, in which trees were removed to simulate preemptive logging management practices. Nine microhabitat characteristics were measured from plot photos revealing differences among ground and canopy microhabitat structure. Small mammals were censused during high (2012) and low (2013) abundant years. Populations of common species were estimated with mark-recapture analysis. Peromyscus spp. were not affected by treatment in either year, but southern red-backed vole populations were greatest in the girdled treatments in 2012 and rarely captured in 2013. Between 6 and 9 mammal species were recorded in all treatments and species composition varied slightly. Estimated species richness was greater in girdled treatments than hemlock controls, but did not differ between girdled and logged treatments, which suggests preemptive logging is as detrimental to some small mammal species as HWA invasion. Overall, there is little evidence of a major shift in small mammal community structure in response to HWA invasion, with only minor changes in relative abundance both years.     

Chromosome substitutions and recombination in the amphiploid Lolium perenne×Festuca pratensis cv Prior (2n=4x=28)

 The synthetic amphiploid cv Prior was created in the early 1970s at the Welsh Plant Breeding Station by crossing colchicine-induced autotetraploids of Lolium perenne (2n=14) and Festuca pratensis (2n=14). Meiosis in the early generations was characterized as stable, with frequent bivalent formation. In situ hybridization of a L. perenne total genomic DNA probe to mitotic chromosome spreads of 12 plants, from two extant populations of Prior, demonstrates extensive recombination between the two genomes. Recombination events occur along the whole length of chromosome arms but with a higher frequency in the medial portion. The species origins of chromosomes were assigned by the presence or absence of a fluorescent probe at the centromere. There has been a substitution of Festuca-origin chromosomes by those of Lolium-origin, resulting in a mean of 17.9 (15–21) Lolium and 9.7 (7–13) Festuca chromosomes per genotype. Mean chromatin length per genotype comprised 62.1% Lolium and 37.9% Festuca. On average 9.3 Lolium (51.1% of those present) and 3.5 Festuca (37.8%) chromosomes had no recombined segments. For chromosomes which did show recombination, fewer alien segments were observed in Lolium than in Festuca chromosomes. Festuca chromosomes in genotypes selected for drought resistance had undergone more recombination than in genotypes from an unselected population, though this difference was not statistically significant for the small sample examined. Received: 16 June 1998 / Accepted: 17 September 1998 RID="1" ID="1" <E5>Present address:</E5> Lithuanian Institute of Agriculture, 5051 Dotnuva-Akademija, Kedainiai, Lithuania RID=" ID=" Communicated by J. W. Snape RID=" ID=" <E5>Correspondence to</E5> P. H. Canter     

Investigation of the ‘double cross’ splitting mechanism of single-crystal diamond under nanoindentation via molecular dynamics simulation

Elucidating the mechanical response of diamond is a difficult task due to its ultrahard nature. Here, we applied a molecular dynamics (MD) method to investigate the mechanical response of single-crystal diamond under nanoindentation. There was no obvious “pop in” phenomenon on the load–depth curve, and the elastic modulus deduced from the curve was 1128 GPa, which was similar to the value obtained from experimental measurements. Results from computed tomography (CT) and the coordination number showed that the distribution of the mismatched C atoms around the deformation zone took the form of a ‘double cross.’ The atoms around the indenter tip could be divided into two zones, a translation zone and a lattice distortion zone, based on their movements. Subsequent first-principles calculations revealed that the C-atom displacement barrier varied significantly with direction, which resulted in shear stress between the two zones and the formation of the double-cross splitting.

Open image in new window

Graphical Abstract The displacement of the atoms around the indenter tip